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				<h3> <b>OriginDB</b> - Getting Started</h3>
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			<h1> Introduction </h1>
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					<i>OriginDB</i> is an application created to faciliate collaboration among researchers in the origin of life field. It includes:
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							A database which stores user entered <strong>reactions</strong>, <strong>references</strong>, and <strong>compounds</strong>
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							An interface to add information to the database and edit information already contained in the database
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							An interface for users to create chemical pathways between compounds using reactions which have been cited from the literature
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					<i>OriginDB</i> was created at Georgia Institute of Technology under the supervision of Nick Hud for The Origins Center. It has been written by Jason Power &lt;power.jg@gmail.com&gt; with contributions from Travis Gockel and Brian Plattenburg. For more information on the project see <a href="http://origindb.googlecode.com"> http://origindb.googlecode.com</a>. <i>OriginDB</i> is free and open source software and all of the information in the database is held under the <a rel="license" href="http://creativecommons.org/licenses/by-sa/3.0/us/"> Creative Commons Attribution-Share Alike 3.0 United States License </a>.
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				<h1> Logging into the Database </h1>
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						In order to browse the database without adding any new information, no username or password is required. If, however, you would like to add new reactions or pathways to the database you must contact the database administrator, Nick Hud, at &lt;SOME ADDRESS&gt; and he will respond as soon as possible.
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						After receiving write access to the database you can now log in and add new reactions as well as create and upload your own pathways. All of the content which you add to the database will be licesensed under the <a rel="license" href="http://creativecommons.org/licenses/by-sa/3.0/us/"> Creative Commons Attribution-Share Alike 3.0 United States License</a>. If you do not agree to have your work released under this license you will be unable to contribute to the <i>OriginDB</i> project.
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				<h1> Adding Information to the Database </h1>
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			<h2> Step 1: Adding a Reference </h2>
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					Before a reaction can be added to the database, the journal reference for that reaction must be entered into the system. This can be done at the add reference screen, accessable by selecting <i>Reference</i> &rarr; <i>Add New Reference</i>, as shown below:
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					This will bring you to the <i>Reference Details</i> screen, where all of the information for a new reference can be entered. These details include the title of the publication, year of publication, author(s), journal of publication (including volume and page numbers), and an abstract for the publication. Any information which is not known can be left blank, and will be stored as unknown (the reference can later be upated to contain more complete information).
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					After entering all of the known information about the reference, the reference can be added to the database by clicking the <i>Add Reference</i> button at the top right. Once a reaction has been entered, it is time to move on to adding the compounds necessaary for the reaction.
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			<h2> Step 2: Adding Compounds </h2>
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					The next step in entering a new reaction into the database is to make sure that all of the compounds required for the reaction are available in the database. To add a compound to the database, go to <i>Compound</i> &rarr; <i>Add New Compound</i>, as shown below:
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					You are now at the <i>Compound Details</i> page. This page allows the user to add compounds, along with any relevant details, to the database, as seen below:
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					Once all of the details of the compound have been input, the compound can be stored to the database by clicking the <i>Add Compound</i> button in the top right. After entering all of the compounds needed for the reaction, it is finally time to move on to adding the reaction itself.
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			<h2> Step 3: Adding the Reaction </h2>
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					The final step is to enter the reaction data at the <i>Reaction Details</i> screen. This screen can be reached through <i>Reaction</i> &rarr; <i>Add new Reaction</i>. On this screen, the compounds which are reactants and products of this reaction can be entered into the appropriate sections, along with a mole percentage or percent yield for each. Then any relevant catalysts for the reaction can be added and entered into the reaction. Next, the reference for this reaction can be searched up and added to the reaction. <b>Please note that a reaction cannot be stored without a related reference</b>. Here is also where the conditions required for the reaction to occur can be entered. Once all of this information is entered correctly, the reaction can safely be stored into the database using the <i>Add Reaction</i> button on the bottom right.
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			<h1> Creating a Pathway </h1>
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				A pathway is a set of connections between reactions which form a plausable chemical pathway from one compound to another compound. In <i>OriginDB</i>, pathways can be built from any of the reactions stored in the system. To access the <i>Pathway Editor</i> window, select <i>View</i> &rarr; <i>View Pathway Visualization</i>, as shown below:
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				The <i>Pathway Editor</i> contains three main sections. The largest section, taking up the top portion of the window is the pathway visuaization pane, which contains a view of the current pathway which can be zoomed, panned, and edited here. The bottom right portion of the screen contains a reaction search filter system, which can be used to search for reactions stored in <i>OriginDB</i> to add to the pathway. To obtain detailed information of any reaction in the currently displayed pathway, simply select it and the details will show up in the reaction details pane. The bottom left section contains the reaction details, which is populated when a reaction is selected either in the pathway visualization pane or in search results list.
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				More details on how to use each portion of the <i>Pathway Editor</i> can be found in the sections below.
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			<h2> Searching for Reactions</h2>
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					One major component of the <i>Pathway Editor</i> is the reaction search system. To search for a reaction, any number of filters can be added based on reactants, product, temperature ranges, reference paper, or any other known piece of information. Any number of filters may be used to further refine the search.
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					Once all of the needed filters are in place, select the <i>Search/Apply Filter</i> button to bring up a list of results on the right-hand side of the window.
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			<h2> Adding a Reaction to the Pathway </h2>
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					Once a suitable reaction has been found via the search portion of the <i>Pathway Editor</i>, it is ready to be added to the current pathway visualization.
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					To add the reaction to the pathway visualization, click the <i>Add to Pathway</i> button above the results list to add it to the pathway. If this is the first reaction in the pathway, this may not be very exciting.
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					Once the pathway has been begun, the user can continue to add reactions to form a complete pathway from one chemical compound to another.
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			<h2> Adding Another Reaction to the Pathway </h2>
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					To add another reaction to the pathway, you can either manually enter information into the filters again or drag and drop information from the reaction details pane. As before, the search results will appear to the right after the <i>Search/Apply Filter</i> button has been pressed. The reactions can now be added to the pathway via the <i>Add to Pathway</i> button above the search results area.
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					When a new reaction is added to an existing pathway, <i>OriginDB</i> will attempt to link it into the exisiting reaction(s) for you. If it finds any matches in the reactants or products of the new reaction and the opposite side of an existing reaction, it will add a color-coded arrow connecting the reactions, as seen below:
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						These arrows can be adjusted or removed, or drawn manually using the tooltips located above the pathway visualization. To neatly organize all of the reactions in the pathway, simply click the <i>Clean Display</i> button.
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			<h2> Uploading Your Pathway to the Database </h2>
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				Not yet implemented.
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